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Series GSE19751 Query DataSets for GSE19751
Status Public on Jan 07, 2010
Title Gene expression effects of morpholino directed spRunt-1 knockdown on hatched blastula stage embryos
Organism Strongylocentrotus purpuratus
Experiment type Expression profiling by array
Summary Runt domain (Runx) transcription factors constitute a metazoan family of sequence specific DNA binding proteins that are essential for animal development. The sea urchin Runx gene SpRunt-1, which is expressed globally during early embryogenesis, is required for blastula stage cell proliferation and subsequently for cell survival. To obtain a comprehensive list of SpRunt-1 regulatory targets we screened a custom microarray representing the blastula stage transcriptome of Strongylocentrotus purpuratus, comparing relative hybridization signals generated by labeled RNA from 18 hr control versus SpRunt-1 morphant embryos.
 
Overall design For an 8x15k chip the 8 arrays were 4 biological replicates
and a dye swap of the same 4.

Biological Replicates -

Four separate embryo cultures, each from a different mating
pair were initiated and divided into a control group and
a treatment group. All of the embryos in the treatment group
were micoinjected with a splice-blocking morpholino
antisense oligonucleotide (MASO) targeted to SpRunt-1.

All control and sample embryos were developed to hatched blastula
stage (18 hours post-fertilization) in filtered seawater at 15°C.
Total RNA was extracted from each of the four separate samples
(3,600 embryos in each sample) with an RNA yield near 5 micro grams
per sample. Total RNA was also extracted from the untreated embryos
of each separate culture pooled together (about 14,400) with an RNA
yield near 20 micro grams.

Technical (dye swap) Replicates -

Control derived Cy3 (green) labeled aRNA was mixed with sample derived
Cy5 (red) labeled aRNA in one biological replicate set of 4 samples and
using half of the extracted RNA amount. The other half of the RNA was
reciprocally labeled with control derived aRNA Cy5 labeled and sample
derived aRNA Cy3 labeled.
 
Contributor(s) Robertson AJ, King B, Coluccio A, Coffman JA
Citation(s) 23789095
Submission date Jan 05, 2010
Last update date Jun 25, 2013
Contact name Anthony James Robertson
E-mail(s) tony@mdibl.org
Phone 207 288-9880
URL http://www.mdibl.org/info/directory.shtml
Organization name Mount Desert Island Biolabs
Department Functional Genomics
Lab James A. Coffman
Street address Box 35 Old Bar Harbor Road
City Salisbury Cove
State/province ME
ZIP/Postal code 04672
Country USA
 
Platforms (1)
GPL9839 Strongylocentrotus purpuratus 8x15k (evidence-based array representing expressed genes from the blastula stage embryo)
Samples (8)
GSM493000 Array_1_reference_control_green_runt_replicate_1_red
GSM493001 Array_2_reference_control_green_runt_replicate_2_red
GSM493191 Array_3_reference_control_green_runt_replicate_3_red
Relations
BioProject PRJNA122219

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19751_RAW.tar 26.1 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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